{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,6,2]],"date-time":"2024-06-02T20:16:12Z","timestamp":1717359372548},"reference-count":73,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2011,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>In the last decades, microarray technology has spread, leading to a dramatic increase of publicly available datasets. The first statistical tools developed were focused on the identification of significant differentially expressed genes. Later, researchers moved toward the systematic integration of gene expression profiles with additional biological information, such as chromosomal location, ontological annotations or sequence features. The analysis of gene expression linked to physical location of genes on chromosomes allows the identification of transcriptionally imbalanced regions, while, Gene Set Analysis focuses on the detection of coordinated changes in transcriptional levels among sets of biologically related genes.<\/jats:p>\n            <jats:p>In this field, meta-analysis offers the possibility to compare different studies, addressing the same biological question to fully exploit public gene expression datasets.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>We describe STEPath, a method that starts from gene expression profiles and integrates the analysis of imbalanced region as an <jats:italic>a priori<\/jats:italic> step before performing gene set analysis. The application of STEPath in individual studies produced gene set scores weighted by chromosomal activation. As a final step, we propose a way to compare these scores across different studies (meta-analysis) on related biological issues. One complication with meta-analysis is batch effects, which occur because molecular measurements are affected by laboratory conditions, reagent lots and personnel differences. Major problems occur when batch effects are correlated with an outcome of interest and lead to incorrect conclusions. We evaluated the power of combining chromosome mapping and gene set enrichment analysis, performing the analysis on a dataset of leukaemia (example of individual study) and on a dataset of skeletal muscle diseases (meta-analysis approach).<\/jats:p>\n            <jats:p>In leukaemia, we identified the Hox gene set, a gene set closely related to the pathology that other algorithms of gene set analysis do not identify, while the meta-analysis approach on muscular disease discriminates between related pathologies and correlates similar ones from different studies.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>STEPath is a new method that integrates gene expression profiles, genomic co-expressed regions and the information about the biological function of genes. The usage of the STEPath-computed gene set scores overcomes batch effects in the meta-analysis approaches allowing the direct comparison of different pathologies and different studies on a gene set activation level.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-12-92","type":"journal-article","created":{"date-parts":[[2011,4,12]],"date-time":"2011-04-12T18:52:13Z","timestamp":1302634333000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Statistical Test of Expression Pattern (STEPath): a new strategy to integrate gene expression data with genomic information in individual and meta-analysis studies"],"prefix":"10.1186","volume":"12","author":[{"given":"Paolo","family":"Martini","sequence":"first","affiliation":[]},{"given":"Davide","family":"Risso","sequence":"additional","affiliation":[]},{"given":"Gabriele","family":"Sales","sequence":"additional","affiliation":[]},{"given":"Chiara","family":"Romualdi","sequence":"additional","affiliation":[]},{"given":"Gerolamo","family":"Lanfranchi","sequence":"additional","affiliation":[]},{"given":"Stefano","family":"Cagnin","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2011,4,11]]},"reference":[{"issue":"3","key":"4474_CR1","first-page":"121","volume":"4","author":"DJ Brennan","year":"2007","unstructured":"Brennan DJ, Kelly C, Rexhepaj E, Dervan PA, Duffy MJ, Gallagher WM: Contribution of DNA and tissue microarray technology to the identification and validation of biomarkers and personalised medicine in breast cancer. Cancer Genomics Proteomics 2007, 4(3):121\u2013134.","journal-title":"Cancer Genomics Proteomics"},{"issue":"8","key":"4474_CR2","first-page":"1927","volume":"63","author":"Y Chen","year":"2003","unstructured":"Chen Y, Miller C, Mosher R, Zhao X, Deeds J, Morrissey M, Bryant B, Yang D, Meyer R, Cronin F, et al.: Identification of cervical cancer markers by cDNA and tissue microarrays. Cancer Res 2003, 63(8):1927\u20131935.","journal-title":"Cancer Res"},{"issue":"3","key":"4474_CR3","doi-asserted-by":"publisher","first-page":"269","DOI":"10.1586\/14737159.7.3.269","volume":"7","author":"DP Malinowski","year":"2007","unstructured":"Malinowski DP: Multiple biomarkers in molecular oncology. II. Molecular diagnostics applications in breast cancer management. Expert Rev Mol Diagn 2007, 7(3):269\u2013280. 10.1586\/14737159.7.3.269","journal-title":"Expert Rev Mol Diagn"},{"issue":"2","key":"4474_CR4","doi-asserted-by":"publisher","first-page":"117","DOI":"10.1586\/14737159.7.2.117","volume":"7","author":"DP Malinowski","year":"2007","unstructured":"Malinowski DP: Multiple biomarkers in molecular oncology. I. Molecular diagnostics applications in cervical cancer detection. Expert Rev Mol Diagn 2007, 7(2):117\u2013131. 10.1586\/14737159.7.2.117","journal-title":"Expert Rev Mol Diagn"},{"issue":"3","key":"4474_CR5","doi-asserted-by":"publisher","first-page":"519","DOI":"10.1016\/j.surg.2004.05.041","volume":"136","author":"JA Olson Jr","year":"2004","unstructured":"Olson JA Jr: Application of microarray profiling to clinical trials in cancer. Surgery 2004, 136(3):519\u2013523. 10.1016\/j.surg.2004.05.041","journal-title":"Surgery"},{"issue":"1","key":"4474_CR6","doi-asserted-by":"publisher","first-page":"30","DOI":"10.1093\/bioinformatics\/btl543","volume":"23","author":"Y Sun","year":"2007","unstructured":"Sun Y, Goodison S, Li J, Liu L, Farmerie W: Improved breast cancer prognosis through the combination of clinical and genetic markers. Bioinformatics 2007, 23(1):30\u201337. 10.1093\/bioinformatics\/btl543","journal-title":"Bioinformatics"},{"key":"4474_CR7","volume-title":"Nucleic Acids Res","author":"T Barrett","year":"2009","unstructured":"Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, Evangelista C, Kim IF, Soboleva A, Tomashevsky M, Marshall KA, et al.: NCBI GEO: archive for high-throughput functional genomic data. Nucleic Acids Res 2009, (37 Database):D885\u2013890. 10.1093\/nar\/gkn764"},{"issue":"4","key":"4474_CR8","doi-asserted-by":"publisher","first-page":"365","DOI":"10.1038\/ng1201-365","volume":"29","author":"A Brazma","year":"2001","unstructured":"Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, et al.: Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet 2001, 29(4):365\u2013371. 10.1038\/ng1201-365","journal-title":"Nat Genet"},{"issue":"10-11","key":"4474_CR9","doi-asserted-by":"publisher","first-page":"1075","DOI":"10.1016\/j.crvi.2003.09.026","volume":"326","author":"P Rocca-Serra","year":"2003","unstructured":"Rocca-Serra P, Brazma A, Parkinson H, Sarkans U, Shojatalab M, Contrino S, Vilo J, Abeygunawardena N, Mukherjee G, Holloway E, et al.: ArrayExpress: a public database of gene expression data at EBI. C R Biol 2003, 326(10\u201311):1075\u20131078. 10.1016\/j.crvi.2003.09.026","journal-title":"C R Biol"},{"issue":"8","key":"4474_CR10","doi-asserted-by":"publisher","first-page":"980","DOI":"10.1093\/bioinformatics\/btm051","volume":"23","author":"JJ Goeman","year":"2007","unstructured":"Goeman JJ, Buhlmann P: Analyzing gene expression data in terms of gene sets: methodological issues. Bioinformatics 2007, 23(8):980\u2013987. 10.1093\/bioinformatics\/btm051","journal-title":"Bioinformatics"},{"key":"4474_CR11","doi-asserted-by":"crossref","unstructured":"Shen K, Tseng GC: Meta-analysis for pathway enrichment analysis when combining multiple genomic studies. Bioinformatics 26(10):1316\u20131323. 10.1093\/bioinformatics\/btq148","DOI":"10.1093\/bioinformatics\/btq148"},{"issue":"3","key":"4474_CR12","doi-asserted-by":"publisher","first-page":"321","DOI":"10.1002\/(SICI)1097-0258(19990215)18:3<321::AID-SIM28>3.0.CO;2-P","volume":"18","author":"SL Normand","year":"1999","unstructured":"Normand SL: Meta-analysis: formulating, evaluating, combining, and reporting. Stat Med 1999, 18(3):321\u2013359. 10.1002\/(SICI)1097-0258(19990215)18:3<321::AID-SIM28>3.0.CO;2-P","journal-title":"Stat Med"},{"issue":"15","key":"4474_CR13","first-page":"4427","volume":"62","author":"DR Rhodes","year":"2002","unstructured":"Rhodes DR, Barrette TR, Rubin MA, Ghosh D, Chinnaiyan AM: Meta-analysis of microarrays: interstudy validation of gene expression profiles reveals pathway dysregulation in prostate cancer. Cancer Res 2002, 62(15):4427\u20134433.","journal-title":"Cancer Res"},{"issue":"9","key":"4474_CR14","doi-asserted-by":"publisher","first-page":"2922","DOI":"10.1158\/1078-0432.CCR-03-0490","volume":"10","author":"G Parmigiani","year":"2004","unstructured":"Parmigiani G, Garrett-Mayer ES, Anbazhagan R, Gabrielson E: A cross-study comparison of gene expression studies for the molecular classification of lung cancer. Clin Cancer Res 2004, 10(9):2922\u20132927. 10.1158\/1078-0432.CCR-03-0490","journal-title":"Clin Cancer Res"},{"key":"4474_CR15","doi-asserted-by":"publisher","first-page":"88","DOI":"10.1186\/1471-2164-8-88","volume":"8","author":"WD Park","year":"2007","unstructured":"Park WD, Stegall MD: A meta-analysis of kidney microarray datasets: investigation of cytokine gene detection and correlation with rt-PCR and detection thresholds. BMC Genomics 2007, 8: 88. 10.1186\/1471-2164-8-88","journal-title":"BMC Genomics"},{"issue":"20","key":"4474_CR16","doi-asserted-by":"publisher","first-page":"2500","DOI":"10.1093\/bioinformatics\/btl424","volume":"22","author":"T Manoli","year":"2006","unstructured":"Manoli T, Gretz N, Grone HJ, Kenzelmann M, Eils R, Brors B: Group testing for pathway analysis improves comparability of different microarray datasets. Bioinformatics 2006, 22(20):2500\u20132506. 10.1093\/bioinformatics\/btl424","journal-title":"Bioinformatics"},{"issue":"21","key":"4474_CR17","doi-asserted-by":"publisher","first-page":"2658","DOI":"10.1093\/bioinformatics\/btl455","volume":"22","author":"A Callegaro","year":"2006","unstructured":"Callegaro A, Basso D, Bicciato S: A locally adaptive statistical procedure (LAP) to identify differentially expressed chromosomal regions. Bioinformatics 2006, 22(21):2658\u20132666. 10.1093\/bioinformatics\/btl455","journal-title":"Bioinformatics"},{"issue":"9","key":"4474_CR18","doi-asserted-by":"publisher","first-page":"2112","DOI":"10.1093\/bioinformatics\/bti183","volume":"21","author":"J Toedling","year":"2005","unstructured":"Toedling J, Schmeier S, Heinig M, Georgi B, Roepcke S: MACAT--microarray chromosome analysis tool. Bioinformatics 2005, 21(9):2112\u20132113. 10.1093\/bioinformatics\/bti183","journal-title":"Bioinformatics"},{"key":"4474_CR19","doi-asserted-by":"publisher","first-page":"526","DOI":"10.1186\/1471-2105-7-526","volume":"7","author":"FE Turkheimer","year":"2006","unstructured":"Turkheimer FE, Roncaroli F, Hennuy B, Herens C, Nguyen M, Martin D, Evrard A, Bours V, Boniver J, Deprez M: Chromosomal patterns of gene expression from microarray data: methodology, validation and clinical relevance in gliomas. BMC Bioinformatics 2006, 7: 526. 10.1186\/1471-2105-7-526","journal-title":"BMC Bioinformatics"},{"issue":"9","key":"4474_CR20","doi-asserted-by":"publisher","first-page":"1943","DOI":"10.1093\/bioinformatics\/bti260","volume":"21","author":"WT Barry","year":"2005","unstructured":"Barry WT, Nobel AB, Wright FA: Significance analysis of functional categories in gene expression studies: a structured permutation approach. Bioinformatics 2005, 21(9):1943\u20131949. 10.1093\/bioinformatics\/bti260","journal-title":"Bioinformatics"},{"issue":"1","key":"4474_CR21","doi-asserted-by":"publisher","first-page":"93","DOI":"10.1093\/bioinformatics\/btg382","volume":"20","author":"JJ Goeman","year":"2004","unstructured":"Goeman JJ, van de Geer SA, de Kort F, van Houwelingen HC: A global test for groups of genes: testing association with a clinical outcome. Bioinformatics 2004, 20(1):93\u201399. 10.1093\/bioinformatics\/btg382","journal-title":"Bioinformatics"},{"issue":"43","key":"4474_CR22","doi-asserted-by":"publisher","first-page":"15545","DOI":"10.1073\/pnas.0506580102","volume":"102","author":"A Subramanian","year":"2005","unstructured":"Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, et al.: Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 2005, 102(43):15545\u201315550. 10.1073\/pnas.0506580102","journal-title":"Proc Natl Acad Sci USA"},{"issue":"38","key":"4474_CR23","doi-asserted-by":"publisher","first-page":"13544","DOI":"10.1073\/pnas.0506577102","volume":"102","author":"L Tian","year":"2005","unstructured":"Tian L, Greenberg SA, Kong SW, Altschuler J, Kohane IS, Park PJ: Discovering statistically significant pathways in expression profiling studies. Proc Natl Acad Sci USA 2005, 102(38):13544\u201313549. 10.1073\/pnas.0506577102","journal-title":"Proc Natl Acad Sci USA"},{"issue":"12","key":"4474_CR24","doi-asserted-by":"publisher","first-page":"2867","DOI":"10.1093\/bioinformatics\/bti417","volume":"21","author":"AM Levin","year":"2005","unstructured":"Levin AM, Ghosh D, Cho KR, Kardia SL: A model-based scan statistic for identifying extreme chromosomal regions of gene expression in human tumors. Bioinformatics 2005, 21(12):2867\u20132874. 10.1093\/bioinformatics\/bti417","journal-title":"Bioinformatics"},{"issue":"Pt 2","key":"4474_CR25","doi-asserted-by":"publisher","first-page":"381","DOI":"10.1093\/brain\/awm312","volume":"131","author":"AN Anderson","year":"2008","unstructured":"Anderson AN, Roncaroli F, Hodges A, Deprez M, Turkheimer FE: Chromosomal profiles of gene expression in Huntington's disease. Brain 2008, 131(Pt 2):381\u2013388. 10.1093\/brain\/awm312","journal-title":"Brain"},{"key":"4474_CR26","doi-asserted-by":"publisher","first-page":"107","DOI":"10.1214\/07-AOAS101","volume":"1","author":"Efron and Tibshirani","year":"2007","unstructured":"Efron and Tibshirani: On testing the significance of sets of genes. Ann Appl Stat 2007, 1: 107\u2013129. 10.1214\/07-AOAS101","journal-title":"Ann Appl Stat"},{"key":"4474_CR27","doi-asserted-by":"crossref","unstructured":"Szabo PM, Tamasi V, Molnar V, Andrasfalvy M, Tombol Z, Farkas R, Kovesdi K, Patocs A, Toth M, Szalai C, et al.: Meta-analysis of adrenocortical tumour genomics data: novel pathogenic pathways revealed. Oncogene 29(21):3163\u20133172. 10.1038\/onc.2010.80","DOI":"10.1038\/onc.2010.80"},{"key":"4474_CR28","doi-asserted-by":"crossref","unstructured":"Sinha B, Bhattacharya D, Sinha DK, Talwar S, Maharana S, Gupta S, Shivashankar GV: Dynamic organization of chromatin assembly and transcription factories in living cells. Methods Cell Biol 98: 57\u201378. full_text","DOI":"10.1016\/S0091-679X(10)98003-5"},{"key":"4474_CR29","doi-asserted-by":"crossref","unstructured":"van Steensel B, Dekker J: Genomics tools for unraveling chromosome architecture. Nat Biotechnol 28(10):1089\u20131095. 10.1038\/nbt.1680","DOI":"10.1038\/nbt.1680"},{"issue":"7126","key":"4474_CR30","doi-asserted-by":"publisher","first-page":"379","DOI":"10.1038\/445379a","volume":"445","author":"KJ Meaburn","year":"2007","unstructured":"Meaburn KJ, Misteli T: Cell biology: chromosome territories. Nature 2007, 445(7126):379\u2013781. 10.1038\/445379a","journal-title":"Nature"},{"issue":"9","key":"4474_CR31","doi-asserted-by":"publisher","first-page":"1106","DOI":"10.1038\/ncb1771","volume":"10","author":"M Ebisuya","year":"2008","unstructured":"Ebisuya M, Yamamoto T, Nakajima M, Nishida E: Ripples from neighbouring transcription. Nat Cell Biol 2008, 10(9):1106\u20131113. 10.1038\/ncb1771","journal-title":"Nat Cell Biol"},{"issue":"9","key":"4474_CR32","doi-asserted-by":"publisher","first-page":"5116","DOI":"10.1073\/pnas.091062498","volume":"98","author":"VG Tusher","year":"2001","unstructured":"Tusher VG, Tibshirani R, Chu G: Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA 2001, 98(9):5116\u20135121. 10.1073\/pnas.091062498","journal-title":"Proc Natl Acad Sci USA"},{"issue":"1","key":"4474_CR33","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1038\/75556","volume":"25","author":"M Ashburner","year":"2000","unstructured":"Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al.: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000, 25(1):25\u201329. 10.1038\/75556","journal-title":"Nat Genet"},{"issue":"1","key":"4474_CR34","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1093\/nar\/28.1.27","volume":"28","author":"M Kanehisa","year":"2000","unstructured":"Kanehisa M, Goto S: KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 2000, 28(1):27\u201330. 10.1093\/nar\/28.1.27","journal-title":"Nucleic Acids Res"},{"key":"4474_CR35","doi-asserted-by":"crossref","unstructured":"Kanehisa M, Goto S, Furumichi M, Tanabe M, Hirakawa M: KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res (38 Database):D355\u2013360.","DOI":"10.1093\/nar\/gkp896"},{"key":"4474_CR36","first-page":"D354","volume-title":"Nucleic Acids Res","author":"M Kanehisa","year":"2006","unstructured":"Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, Kawashima S, Katayama T, Araki M, Hirakawa M: From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 2006, (34 Database):D354\u2013357. 10.1093\/nar\/gkj102"},{"issue":"19","key":"4474_CR37","doi-asserted-by":"publisher","first-page":"6083","DOI":"10.1093\/nar\/gki892","volume":"33","author":"PD Karp","year":"2005","unstructured":"Karp PD, Ouzounis CA, Moore-Kochlacs C, Goldovsky L, Kaipa P, Ahren D, Tsoka S, Darzentas N, Kunin V, Lopez-Bigas N: Expansion of the BioCyc collection of pathway\/genome databases to 160 genomes. Nucleic Acids Res 2005, 33(19):6083\u20136089. 10.1093\/nar\/gki892","journal-title":"Nucleic Acids Res"},{"key":"4474_CR38","unstructured":"BioCarta[http:\/\/www.biocarta.com]"},{"key":"4474_CR39","unstructured":"SuperArray[http:\/\/www.sabiosciences.com\/pathwaycentral.php]"},{"key":"4474_CR40","unstructured":"WikiPathways[http:\/\/www.wikipathways.org]"},{"key":"4474_CR41","doi-asserted-by":"publisher","first-page":"502","DOI":"10.1186\/1471-2105-9-502","volume":"9","author":"S Song","year":"2008","unstructured":"Song S, Black MA: Microarray-based gene set analysis: a comparison of current methods. BMC Bioinformatics 2008, 9: 502. 10.1186\/1471-2105-9-502","journal-title":"BMC Bioinformatics"},{"key":"4474_CR42","first-page":"289","volume-title":"J R Statist Soc B","author":"Y Benjamini","year":"1995","unstructured":"Benjamini Y, Hochberg Y: Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Statist Soc B 1995, 289\u2013300."},{"key":"4474_CR43","doi-asserted-by":"crossref","unstructured":"Sales G, Coppe A, Bicciato S, Bortoluzzi S, Romualdi C: Impact of probe annotation on the integration of miRNA-mRNA expression profiles for miRNA target detection. Nucleic Acids Res 38(7):e97. 10.1093\/nar\/gkp1239","DOI":"10.1093\/nar\/gkp1239"},{"issue":"20","key":"4474_CR44","doi-asserted-by":"publisher","first-page":"e175","DOI":"10.1093\/nar\/gni179","volume":"33","author":"M Dai","year":"2005","unstructured":"Dai M, Wang P, Boyd AD, Kostov G, Athey B, Jones EG, Bunney WE, Myers RM, Speed TP, Akil H, et al.: Evolving gene\/transcript definitions significantly alter the interpretation of GeneChip data. Nucleic Acids Res 2005, 33(20):e175. 10.1093\/nar\/gni179","journal-title":"Nucleic Acids Res"},{"issue":"2","key":"4474_CR45","doi-asserted-by":"publisher","first-page":"249","DOI":"10.1093\/biostatistics\/4.2.249","volume":"4","author":"RA Irizarry","year":"2003","unstructured":"Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP: Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 2003, 4(2):249\u2013264. 10.1093\/biostatistics\/4.2.249","journal-title":"Biostatistics"},{"issue":"11","key":"4474_CR46","doi-asserted-by":"publisher","first-page":"823","DOI":"10.1038\/nrc2253","volume":"7","author":"AV Krivtsov","year":"2007","unstructured":"Krivtsov AV, Armstrong SA: MLL translocations, histone modifications and leukaemia stem-cell development. Nat Rev Cancer 2007, 7(11):823\u2013833. 10.1038\/nrc2253","journal-title":"Nat Rev Cancer"},{"key":"4474_CR47","doi-asserted-by":"publisher","first-page":"36","DOI":"10.1186\/1755-8794-2-36","volume":"2","author":"A Zangrando","year":"2009","unstructured":"Zangrando A, Dell'orto MC, Te Kronnie G, Basso G: MLL rearrangements in pediatric acute lymphoblastic and myeloblastic leukemias: MLL specific and lineage specific signatures. BMC Med Genomics 2009, 2: 36. 10.1186\/1755-8794-2-36","journal-title":"BMC Med Genomics"},{"issue":"10","key":"4474_CR48","doi-asserted-by":"crossref","first-page":"3801","DOI":"10.1182\/blood.V89.10.3801","volume":"89","author":"JM Hilden","year":"1997","unstructured":"Hilden JM, Smith FO, Frestedt JL, McGlennen R, Howells WB, Sorensen PH, Arthur DC, Woods WG, Buckley J, Bernstein ID, et al.: MLL gene rearrangement, cytogenetic 11q23 abnormalities, and expression of the NG2 molecule in infant acute myeloid leukemia. Blood 1997, 89(10):3801\u20133805.","journal-title":"Blood"},{"issue":"10","key":"4474_CR49","doi-asserted-by":"publisher","first-page":"6567","DOI":"10.1073\/pnas.082099299","volume":"99","author":"R Tibshirani","year":"2002","unstructured":"Tibshirani R, Hastie T, Narasimhan B, Chu G: Diagnosis of multiple cancer types by shrunken centroids of gene expression. Proc Natl Acad Sci USA 2002, 99(10):6567\u20136572. 10.1073\/pnas.082099299","journal-title":"Proc Natl Acad Sci USA"},{"issue":"19","key":"4474_CR50","doi-asserted-by":"publisher","first-page":"2373","DOI":"10.1093\/bioinformatics\/btl401","volume":"22","author":"SW Kong","year":"2006","unstructured":"Kong SW, Pu WT, Park PJ: A multivariate approach for integrating genome-wide expression data and biological knowledge. Bioinformatics 2006, 22(19):2373\u20132380. 10.1093\/bioinformatics\/btl401","journal-title":"Bioinformatics"},{"issue":"1","key":"4474_CR51","doi-asserted-by":"publisher","first-page":"262","DOI":"10.1182\/blood-2002-10-3221","volume":"102","author":"AA Ferrando","year":"2003","unstructured":"Ferrando AA, Armstrong SA, Neuberg DS, Sallan SE, Silverman LB, Korsmeyer SJ, Look AT: Gene expression signatures in MLL-rearranged T-lineage and B-precursor acute leukemias: dominance of HOX dysregulation. Blood 2003, 102(1):262\u2013268. 10.1182\/blood-2002-10-3221","journal-title":"Blood"},{"issue":"47","key":"4474_CR52","doi-asserted-by":"publisher","first-page":"6766","DOI":"10.1038\/sj.onc.1210760","volume":"26","author":"B Argiropoulos","year":"2007","unstructured":"Argiropoulos B, Humphries RK: Hox genes in hematopoiesis and leukemogenesis. Oncogene 2007, 26(47):6766\u20136776. 10.1038\/sj.onc.1210760","journal-title":"Oncogene"},{"issue":"Pt 4","key":"4474_CR53","doi-asserted-by":"publisher","first-page":"996","DOI":"10.1093\/brain\/awl023","volume":"129","author":"M Bakay","year":"2006","unstructured":"Bakay M, Wang Z, Melcon G, Schiltz L, Xuan J, Zhao P, Sartorelli V, Seo J, Pegoraro E, Angelini C, et al.: Nuclear envelope dystrophies show a transcriptional fingerprint suggesting disruption of Rb-MyoD pathways in muscle regeneration. Brain 2006, 129(Pt 4):996\u20131013. 10.1093\/brain\/awl023","journal-title":"Brain"},{"issue":"11","key":"4474_CR54","doi-asserted-by":"publisher","first-page":"e3750","DOI":"10.1371\/journal.pone.0003750","volume":"3","author":"A Saenz","year":"2008","unstructured":"Saenz A, Azpitarte M, Armananzas R, Leturcq F, Alzualde A, Inza I, Garcia-Bragado F, De la Herran G, Corcuera J, Cabello A, et al.: Gene expression profiling in limb-girdle muscular dystrophy 2A. PLoS One 2008, 3(11):e3750. 10.1371\/journal.pone.0003750","journal-title":"PLoS One"},{"issue":"2","key":"4474_CR55","doi-asserted-by":"publisher","first-page":"171","DOI":"10.1093\/bioinformatics\/bth469","volume":"21","author":"L Ein-Dor","year":"2005","unstructured":"Ein-Dor L, Kela I, Getz G, Givol D, Domany E: Outcome signature genes in breast cancer: is there a unique set? Bioinformatics 2005, 21(2):171\u2013178. 10.1093\/bioinformatics\/bth469","journal-title":"Bioinformatics"},{"issue":"19","key":"4474_CR56","doi-asserted-by":"publisher","first-page":"5676","DOI":"10.1093\/nar\/gkg763","volume":"31","author":"PK Tan","year":"2003","unstructured":"Tan PK, Downey TJ, Spitznagel EL Jr, Xu P, Fu D, Dimitrov DS, Lempicki RA, Raaka BM, Cam MC: Evaluation of gene expression measurements from commercial microarray platforms. Nucleic Acids Res 2003, 31(19):5676\u20135684. 10.1093\/nar\/gkg763","journal-title":"Nucleic Acids Res"},{"issue":"25","key":"4474_CR57","doi-asserted-by":"publisher","first-page":"14863","DOI":"10.1073\/pnas.95.25.14863","volume":"95","author":"MB Eisen","year":"1998","unstructured":"Eisen MB, Spellman PT, Brown PO, Botstein D: Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 1998, 95(25):14863\u201314868. 10.1073\/pnas.95.25.14863","journal-title":"Proc Natl Acad Sci USA"},{"issue":"26","key":"4474_CR58","doi-asserted-by":"publisher","first-page":"3283","DOI":"10.1093\/hmg\/11.26.3283","volume":"11","author":"S Campanaro","year":"2002","unstructured":"Campanaro S, Romualdi C, Fanin M, Celegato B, Pacchioni B, Trevisan S, Laveder P, De Pitta C, Pegoraro E, Hayashi YK, et al.: Gene expression profiling in dysferlinopathies using a dedicated muscle microarray. Hum Mol Genet 2002, 11(26):3283\u20133298. 10.1093\/hmg\/11.26.3283","journal-title":"Hum Mol Genet"},{"key":"4474_CR59","doi-asserted-by":"publisher","first-page":"630","DOI":"10.1186\/1471-2164-9-630","volume":"9","author":"E Calura","year":"2008","unstructured":"Calura E, Cagnin S, Raffaello A, Laveder P, Lanfranchi G, Romualdi C: Meta-analysis of expression signatures of muscle atrophy: gene interaction networks in early and late stages. BMC Genomics 2008, 9: 630. 10.1186\/1471-2164-9-630","journal-title":"BMC Genomics"},{"issue":"17","key":"4474_CR60","doi-asserted-by":"publisher","first-page":"3194","DOI":"10.1093\/hmg\/ddp257","volume":"18","author":"I Kramerova","year":"2009","unstructured":"Kramerova I, Kudryashova E, Wu B, Germain S, Vandenborne K, Romain N, Haller RG, Verity MA, Spencer MJ: Mitochondrial abnormalities, energy deficit and oxidative stress are features of calpain 3 deficiency in skeletal muscle. Hum Mol Genet 2009, 18(17):3194\u20133205. 10.1093\/hmg\/ddp257","journal-title":"Hum Mol Genet"},{"issue":"5","key":"4474_CR61","doi-asserted-by":"publisher","first-page":"1476","DOI":"10.2353\/ajpath.2008.080098","volume":"173","author":"A Kesari","year":"2008","unstructured":"Kesari A, Fukuda M, Knoblach S, Bashir R, Nader GA, Rao D, Nagaraju K, Hoffman EP: Dysferlin deficiency shows compensatory induction of Rab27A\/Slp2a that may contribute to inflammatory onset. Am J Pathol 2008, 173(5):1476\u20131487. 10.2353\/ajpath.2008.080098","journal-title":"Am J Pathol"},{"issue":"3","key":"4474_CR62","doi-asserted-by":"publisher","first-page":"774","DOI":"10.2353\/ajpath.2008.070327","volume":"172","author":"K Nagaraju","year":"2008","unstructured":"Nagaraju K, Rawat R, Veszelovszky E, Thapliyal R, Kesari A, Sparks S, Raben N, Plotz P, Hoffman EP: Dysferlin deficiency enhances monocyte phagocytosis: a model for the inflammatory onset of limb-girdle muscular dystrophy 2B. Am J Pathol 2008, 172(3):774\u2013785. 10.2353\/ajpath.2008.070327","journal-title":"Am J Pathol"},{"issue":"21","key":"4474_CR63","doi-asserted-by":"publisher","first-page":"18200","DOI":"10.1074\/jbc.M102009200","volume":"276","author":"DJ Hackam","year":"2001","unstructured":"Hackam DJ, Botelho RJ, Sjolin C, Rotstein OD, Robinson JM, Schreiber AD, Grinstein S: Indirect role for COPI in the completion of FCgamma receptor-mediated phagocytosis. J Biol Chem 2001, 276(21):18200\u201318208. 10.1074\/jbc.M102009200","journal-title":"J Biol Chem"},{"issue":"10","key":"4474_CR64","doi-asserted-by":"publisher","first-page":"RESEARCH0042","DOI":"10.1186\/gb-2001-2-10-research0042","volume":"2","author":"P Pavlidis","year":"2001","unstructured":"Pavlidis P, Noble WS: Analysis of strain and regional variation in gene expression in mouse brain. Genome Biol 2001, 2(10):RESEARCH0042. 10.1186\/gb-2001-2-10-research0042","journal-title":"Genome Biol"},{"issue":"12","key":"4474_CR65","doi-asserted-by":"publisher","first-page":"913","DOI":"10.1016\/j.nmd.2008.08.005","volume":"18","author":"JS Beckmann","year":"2008","unstructured":"Beckmann JS, Spencer M: Calpain 3, the \"gatekeeper\" of proper sarcomere assembly, turnover and maintenance. Neuromuscul Disord 2008, 18(12):913\u2013921. 10.1016\/j.nmd.2008.08.005","journal-title":"Neuromuscul Disord"},{"issue":"6","key":"4474_CR66","doi-asserted-by":"publisher","first-page":"721","DOI":"10.1038\/sj.ejhg.5201414","volume":"13","author":"Y Huang","year":"2005","unstructured":"Huang Y, Verheesen P, Roussis A, Frankhuizen W, Ginjaar I, Haldane F, Laval S, Anderson LV, Verrips T, Frants RR, et al.: Protein studies in dysferlinopathy patients using llama-derived antibody fragments selected by phage display. Eur J Hum Genet 2005, 13(6):721\u2013730. 10.1038\/sj.ejhg.5201414","journal-title":"Eur J Hum Genet"},{"issue":"10","key":"4474_CR67","doi-asserted-by":"publisher","first-page":"R80","DOI":"10.1186\/gb-2004-5-10-r80","volume":"5","author":"RC Gentleman","year":"2004","unstructured":"Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, et al.: Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 2004, 5(10):R80. 10.1186\/gb-2004-5-10-r80","journal-title":"Genome Biol"},{"issue":"3","key":"4474_CR68","doi-asserted-by":"publisher","first-page":"307","DOI":"10.1093\/bioinformatics\/btg405","volume":"20","author":"L Gautier","year":"2004","unstructured":"Gautier L, Cope L, Bolstad BM, Irizarry RA: affy--analysis of Affymetrix GeneChip data at the probe level. Bioinformatics 2004, 20(3):307\u2013315. 10.1093\/bioinformatics\/btg405","journal-title":"Bioinformatics"},{"key":"4474_CR69","volume-title":"R: A Language and Environment for Statistical Computing","author":"Team RDC","year":"2009","unstructured":"Team RDC: R: A Language and Environment for Statistical Computing. 2009."},{"key":"4474_CR70","unstructured":"Bolstad BM: preprocessCore: A collection of pre-processing functions."},{"issue":"14","key":"4474_CR71","doi-asserted-by":"publisher","first-page":"1781","DOI":"10.1093\/bioinformatics\/btg252","volume":"19","author":"G Firneisz","year":"2003","unstructured":"Firneisz G, Zehavi I, Vermes C, Hanyecz A, Frieman JA, Glant TT: Identification and quantification of disease-related gene clusters. Bioinformatics 2003, 19(14):1781\u20131786. 10.1093\/bioinformatics\/btg252","journal-title":"Bioinformatics"},{"issue":"5079","key":"4474_CR72","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1126\/science.1439767","volume":"258","author":"CJ Farr","year":"1992","unstructured":"Farr CJ, Goodfellow PN: Hidden messages in genetic maps. Science 1992, 258(5079):49. 10.1126\/science.1439767","journal-title":"Science"},{"issue":"2","key":"4474_CR73","doi-asserted-by":"crossref","first-page":"374","DOI":"10.2144\/03342mt01","volume":"34","author":"AI Saeed","year":"2003","unstructured":"Saeed AI, Sharov V, White J, Li J, Liang W, Bhagabati N, Braisted J, Klapa M, Currier T, Thiagarajan M, et al.: TM4: a free, open-source system for microarray data management and analysis. Biotechniques 2003, 34(2):374\u2013378.","journal-title":"Biotechniques"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-12-92.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T13:37:03Z","timestamp":1630503423000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-12-92"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,4,11]]},"references-count":73,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2011,12]]}},"alternative-id":["4474"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-12-92","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2011,4,11]]},"assertion":[{"value":"8 October 2010","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"11 April 2011","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"11 April 2011","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"92"}}